JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded...

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index a93f233..b77fc47 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -28,7 +28,9 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
@@ -238,6 +240,21 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                     dbVersion, (chid == null ? id : id + chid));
             // dbentry.setMap()
             pdbcs.addDBRef(dbentry);
+            // update any feature groups
+            List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+            List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+            if (allsf!=null && allsf.size()>0)
+            {
+              for (SequenceFeature f:allsf)
+              {
+                if (file.equals(f.getFeatureGroup()))
+                {
+                  f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+                }
+                newsf.add(f);
+              }
+              pdbcs.setSequenceFeatures(newsf);
+            }
           }
         }
         else